Hi all
Please try it out! Make sure to use the proper scripts to get the new
masses, do not just increase time step to 4 fs !
We are writing a paper on this and will share it with everyone when we
have a good draft.
adrian
On 3/12/14 9:55 AM, Thomas Cheatham wrote:
>>> Note AMBER 14 will also support hydrogen mass
>>> repartitioning so in principal you can run at 4fs time step.
>> How much to we really know about this option? I've been playing with it for
> We have been running a DNA 18-mer and also a RNA tetranucleotide r(GACC)
> with h-mass repartitioning on the solute only and on everything. From
> initial analysis, conformational distributions appear fairly identical for
> the r(GACC), however we still need to look at kinetics, water properties
> (viscosity should be higher), etc. When Christina, Ros and I get it
> further analyzed, I'll summarize to the dev list...
>
>> Blue Waters (say) to run lots of simulations at 1, 2 and 4 fs time steps?
>> Has anyone compared 2 and 4 fs where both have the mass repartitioning?
> Ros/Christina, maybe we should fire up some more as per above. --tom
>
>
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--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Mar 12 2014 - 09:00:02 PDT
